1
|
Zait Y, Joseph A, Assmann SM. Stomatal responses to VPD utilize guard cell intracellular signaling components. Front Plant Sci 2024; 15:1351612. [PMID: 38375078 PMCID: PMC10875092 DOI: 10.3389/fpls.2024.1351612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/17/2024] [Indexed: 02/21/2024]
Abstract
Stomatal pores, vital for CO2 uptake and water loss regulation in plants, are formed by two specialized guard cells. Despite their importance, there is limited understanding of how guard cells sense and respond to changes in vapor pressure difference (VPD). This study leverages a selection of CO2 hyposensitive and abscisic acid (ABA) signaling mutants in Arabidopsis, including heterotrimeric G protein mutants and RLK (receptor-like kinase) mutants, along with a variety of canola cultivars to delve into the intracellular signaling mechanisms prompting stomatal closure in response to high VPD. Stomatal conductance response to step changes in VPD was measured using the LI-6800F gas exchange system. Our findings highlight that stomatal responses to VPD utilize intracellular signaling components. VPD hyposensitivity was particularly evident in mutants of the ht1 (HIGH LEAF TEMPERATURE1) gene, which encodes a protein kinase expressed mainly in guard cells, and in gpa1-3, a null mutant of the sole canonical heterotrimeric Gα subunit, previously implicated in stomatal signaling. Consequently, this research identifies a nexus in the intricate relationships between guard cell signal perception, stomatal conductance, environmental humidity, and CO2 levels.
Collapse
Affiliation(s)
- Yotam Zait
- Biology Department, Penn State University, Mueller Laboratory, University Park, PA, United States
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ariel Joseph
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sarah M. Assmann
- Biology Department, Penn State University, Mueller Laboratory, University Park, PA, United States
| |
Collapse
|
2
|
Ferrero-Serrano Á, Chakravorty D, Kirven KJ, Assmann SM. Oryza CLIMtools: A Genome-Environment Association Resource Reveals Adaptive Roles for Heterotrimeric G Proteins in the Regulation of Rice Agronomic Traits. Plant Commun 2024:100813. [PMID: 38213027 DOI: 10.1016/j.xplc.2024.100813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 10/12/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To this end, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that allow the user to: i) explore the local environments of traditional rice varieties (landraces) in South-Eastern Asia, and; ii) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We exemplify the value of these resources, identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior QTL analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing Potential Evapotranspiration gradient and their regulation of key agronomic traits including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce crops that are climate resilient.
Collapse
Affiliation(s)
- Ángel Ferrero-Serrano
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
| | - David Chakravorty
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Kobie J Kirven
- Intercollege Graduate Degree Program in Bioinformatics and Genomics, Pennsylvania State University
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
| |
Collapse
|
3
|
McKinley LN, Kern RG, Assmann SM, Bevilacqua PC. Flanking Sequence Cotranscriptionally Regulates Twister Ribozyme Activity. Biochemistry 2024; 63:53-68. [PMID: 38134329 DOI: 10.1021/acs.biochem.3c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Small nucleolytic ribozymes are RNAs that cleave their own phosphodiester backbone. While proteinaceous enzymes are regulated by a variety of known mechanisms, methods of regulation for ribozymes remain unclear. Twister is one ribozyme class for which many structural and catalytic properties have been elucidated. However, few studies have analyzed the activity of twister ribozymes in the context of a native flanking sequence, even though ribozymes as transcribed in nature do not exist in isolation. Interactions between the ribozyme and its neighboring sequences can induce conformational changes that inhibit self-cleavage, providing a regulatory mechanism that could naturally determine ribozyme activity in vivo and in synthetic applications. To date, eight twister ribozymes have been identified within the staple crop rice (Oryza sativa). Herein, we select several twister ribozymes from rice and show that they are differentially regulated by their flanking sequence using published RNA-seq data sets, structure probing, and cotranscriptional cleavage assays. We found that the Osa 1-2 ribozyme does not interact with its flanking sequences. However, sequences flanking the Osa 1-3 and Osa 1-8 ribozymes form inactive conformations, referred to here as "ribozymogens", that attenuate ribozyme self-cleavage activity. For the Osa 1-3 ribozyme, we show that activity can be rescued upon addition of a complementary antisense oligonucleotide, suggesting ribozymogens can be controlled via external signals. In all, our data provide a plausible mechanism wherein flanking sequence differentially regulates ribozyme activity in vivo. More broadly, the ability to regulate ribozyme behavior locally has potential applications in control of gene expression and synthetic biology.
Collapse
Affiliation(s)
- Lauren N McKinley
- Depatment of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Reuben G Kern
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sarah M Assmann
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Depatment of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| |
Collapse
|
4
|
Ferrero-Serrano Á, Chakravorty D, Kirven KJ, Assmann SM. Oryza CLIMtools: A Genome-Environment Association Resource Reveals Adaptive Roles for Heterotrimeric G Proteins in the Regulation of Rice Agronomic Traits. bioRxiv 2023:2023.05.10.540241. [PMID: 37214799 PMCID: PMC10197702 DOI: 10.1101/2023.05.10.540241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity. To this end, we present Oryza CLIMtools (https://gramene.org/CLIMtools/oryza_v1.0/), the first resource for pan-genome prediction of climate-associated genetic variants in a crop species. Oryza CLIMtools consists of interactive web-based databases that allow the user to: i) explore the local environments of traditional rice varieties (landraces) in South-Eastern Asia, and; ii) investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Genomes Project. We exemplify the value of these resources, identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1. Prior QTL analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing Potential Evapotranspiration gradient and their regulation of key agronomic traits including plant height and seed and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce crops that are climate resilient.
Collapse
Affiliation(s)
- Ángel Ferrero-Serrano
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - David Chakravorty
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Kobie J. Kirven
- Intercollege Graduate Degree Program in Bioinformatics and Genomics, Pennsylvania State University
| | - Sarah M. Assmann
- Biology Department, Pennsylvania State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| |
Collapse
|
5
|
Gookin TE, Chakravorty D, Assmann SM. Influence of expression and purification protocols on Gα biochemical activity: kinetics of plant and mammalian G protein cycles. bioRxiv 2023:2023.05.10.540258. [PMID: 37214830 PMCID: PMC10197700 DOI: 10.1101/2023.05.10.540258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Heterotrimeric G proteins, composed of Gα, Gβ, and Gγ subunits, are a class of signal transduction complexes with broad roles in human health and agriculturally relevant plant physiological and developmental traits. In the classic paradigm, guanine nucleotide binding to the Gα subunit regulates the activation status of the complex. We sought to develop improved methods for heterologous expression and rapid purification of Gα subunits. Using GPA1, the sole canonical Gα subunit of the model plant species, Arabidopsis thaliana, we observed that, compared to conventional purification methods, rapid StrepII-tag mediated purification facilitates isolation of protein with increased GTP binding and hydrolysis activities. Human GNAI1 purified using our approach also displayed the expected binding and hydrolysis activities, indicating our protocol is applicable to mammalian Gα subunits, potentially including those for which purification of enzymatically active protein has been historically problematic. We subsequently utilized domain swaps of GPA1 and human GNAO1 to demonstrate that the inherent instability of GPA1 is a function of the interaction between the Ras and helical domains. Additionally, we found that GPA1-GNAO1 domain swaps partially uncouple the instability from the rapid nucleotide binding kinetics displayed by GPA1.
Collapse
Affiliation(s)
- Timothy E. Gookin
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - David Chakravorty
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sarah M. Assmann
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| |
Collapse
|
6
|
Cantos CF, dePamphilis CW, Assmann SM. Extra-large G proteins have extra-large effects on agronomic traits and stress tolerance in maize and rice. Trends Plant Sci 2023; 28:1033-1044. [PMID: 37156701 PMCID: PMC10524845 DOI: 10.1016/j.tplants.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 05/10/2023]
Abstract
Heterotrimeric G proteins - comprising Gα, Gβ, and Gγ subunits - are ubiquitous elements in eukaryotic cell signaling. Plant genomes contain both canonical Gα subunit genes and a family of plant-specific extra-large G protein genes (XLGs) that encode proteins consisting of a domain with Gα-like features downstream of a long N-terminal domain. In this review we summarize phenotypes modulated by the canonical Gα and XLG proteins of arabidopsis and highlight recent studies in maize and rice that reveal dramatic phenotypic consequences of XLG clustered regularly interspaced short palindromic repeats (CRISPR) mutagenesis in these important crop species. XLGs have both redundant and specific roles in the control of agronomically relevant plant architecture and resistance to both abiotic and biotic stresses. We also point out areas of current controversy, suggest future research directions, and propose a revised, phylogenetically-based nomenclature for XLG protein genes.
Collapse
Affiliation(s)
- Christian F Cantos
- Biology Department, Penn State University, University Park, State College, PA, USA; Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, USA
| | - Claude W dePamphilis
- Biology Department, Penn State University, University Park, State College, PA, USA; Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, State College, PA, USA; Intercollege Graduate Degree Program in Plant Biology, Penn State University, University Park, State College, PA, USA.
| |
Collapse
|
7
|
Assmann SM, Chou HL, Bevilacqua PC. Rock, scissors, paper: How RNA structure informs function. Plant Cell 2023; 35:1671-1707. [PMID: 36747354 DOI: 10.1093/plcell/koad026] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/05/2023] [Accepted: 01/30/2023] [Indexed: 05/30/2023]
Abstract
RNA can fold back on itself to adopt a wide range of structures. These range from relatively simple hairpins to intricate 3D folds and can be accompanied by regulatory interactions with both metabolites and macromolecules. The last 50 yr have witnessed elucidation of an astonishing array of RNA structures including transfer RNAs, ribozymes, riboswitches, the ribosome, the spliceosome, and most recently entire RNA structuromes. These advances in RNA structural biology have deepened insight into fundamental biological processes including gene editing, transcription, translation, and structure-based detection and response to temperature and other environmental signals. These discoveries reveal that RNA can be relatively static, like a rock; that it can have catalytic functions of cutting bonds, like scissors; and that it can adopt myriad functional shapes, like paper. We relate these extraordinary discoveries in the biology of RNA structure to the plant way of life. We trace plant-specific discovery of ribozymes and riboswitches, alternative splicing, organellar ribosomes, thermometers, whole-transcriptome structuromes and pan-structuromes, and conclude that plants have a special set of RNA structures that confer unique types of gene regulation. We finish with a consideration of future directions for the RNA structure-function field.
Collapse
Affiliation(s)
- Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
8
|
Abstract
Biological systems contain a large number of molecules that have diverse interactions. A fruitful path to understanding these systems is to represent them with interaction networks, and then describe flow processes in the network with a dynamic model. Boolean modeling, the simplest discrete dynamic modeling framework for biological networks, has proven its value in recapitulating experimental results and making predictions. A first step and major roadblock to the widespread use of Boolean networks in biology is the laborious network inference and construction process. Here we present a streamlined network inference method that combines the discovery of a parsimonious network structure and the identification of Boolean functions that determine the dynamics of the system. This inference method is based on a causal logic analysis method that associates a logic type (sufficient or necessary) to node-pair relationships (whether promoting or inhibitory). We use the causal logic framework to assimilate indirect information obtained from perturbation experiments and infer relationships that have not yet been documented experimentally. We apply this inference method to a well-studied process of hormone signaling in plants, the signaling underlying abscisic acid (ABA)—induced stomatal closure. Applying the causal logic inference method significantly reduces the manual work typically required for network and Boolean model construction. The inferred model agrees with the manually curated model. We also test this method by re-inferring a network representing epithelial to mesenchymal transition based on a subset of the information that was initially used to construct the model. We find that the inference method performs well for various likely scenarios of inference input information. We conclude that our method is an effective approach toward inference of biological networks and can become an efficient step in the iterative process between experiments and computations.
Collapse
Affiliation(s)
- Parul Maheshwari
- Department of Physics, Penn State University, University Park, PA, United States
- *Correspondence: Parul Maheshwari, ; Reka Albert,
| | - Sarah M. Assmann
- Biology Department, Penn State University, University Park, PA, United States
| | - Reka Albert
- Department of Physics, Penn State University, University Park, PA, United States
- Biology Department, Penn State University, University Park, PA, United States
- *Correspondence: Parul Maheshwari, ; Reka Albert,
| |
Collapse
|
9
|
Ferrero-Serrano Á, Sylvia MM, Forstmeier PC, Olson AJ, Ware D, Bevilacqua PC, Assmann SM. Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis. Genome Biol 2022; 23:101. [PMID: 35440059 PMCID: PMC9017077 DOI: 10.1186/s13059-022-02656-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background Genome-wide association studies (GWAS) aim to correlate phenotypic changes with genotypic variation. Upon transcription, single nucleotide variants (SNVs) may alter mRNA structure, with potential impacts on transcript stability, macromolecular interactions, and translation. However, plant genomes have not been assessed for the presence of these structure-altering polymorphisms or “riboSNitches.” Results We experimentally demonstrate the presence of riboSNitches in transcripts of two Arabidopsis genes, ZINC RIBBON 3 (ZR3) and COTTON GOLGI-RELATED 3 (CGR3), which are associated with continentality and temperature variation in the natural environment. These riboSNitches are also associated with differences in the abundance of their respective transcripts, implying a role in regulating the gene's expression in adaptation to local climate conditions. We then computationally predict riboSNitches transcriptome-wide in mRNAs of 879 naturally inbred Arabidopsis accessions. We characterize correlations between SNPs/riboSNitches in these accessions and 434 climate descriptors of their local environments, suggesting a role of these variants in local adaptation. We integrate this information in CLIMtools V2.0 and provide a new web resource, T-CLIM, that reveals associations between transcript abundance variation and local environmental variation. Conclusion We functionally validate two plant riboSNitches and, for the first time, demonstrate riboSNitch conditionality dependent on temperature, coining the term “conditional riboSNitch.” We provide the first pan-genome-wide prediction of riboSNitches in plants. We expand our previous CLIMtools web resource with riboSNitch information and with 1868 additional Arabidopsis genomes and 269 additional climate conditions, which will greatly facilitate in silico studies of natural genetic variation, its phenotypic consequences, and its role in local adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02656-4.
Collapse
Affiliation(s)
- Ángel Ferrero-Serrano
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| | - Megan M Sylvia
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Peter C Forstmeier
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Andrew J Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Philip C Bevilacqua
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, State College, PA, 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA. .,Center for RNA Molecular Biology, Pennsylvania State University, University Park, State College, PA, 16802, USA.
| |
Collapse
|
10
|
Abstract
RNA interactions are exceptionally strong and highly redundant. As such, nearly any two RNAs have the potential to interact with one another over relatively short stretches, especially at high RNA concentrations. This is especially true for pairs of RNAs that do not form strong self-structure. Such phenomena can drive liquid-liquid phase separation, either solely from RNA-RNA interactions in the presence of divalent or organic cations, or in concert with proteins. RNA interactions can drive multimerization of RNA strands via both base-pairing and tertiary interactions. In this article, we explore the tendency of RNA to form stable monomers, dimers, and higher order structures as a function of RNA length and sequence through a focus on the intrinsic thermodynamic, kinetic, and structural properties of RNA. The principles we discuss are independent of any specific type of biomolecular condensate, and thus widely applicable. We also speculate how external conditions experienced by living organisms can influence the formation of nonmembranous compartments, again focusing on the physical and structural properties of RNA. Plants, in particular, are subject to diverse abiotic stresses including extreme temperatures, drought, and salinity. These stresses and the cellular responses to them, including changes in the concentrations of small molecules such as polyamines, salts, and compatible solutes, have the potential to regulate condensate formation by melting or strengthening base-pairing. Reversible condensate formation, perhaps including regulation by circadian rhythms, could impact biological processes in plants, and other organisms.
Collapse
Affiliation(s)
- Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Allison M Williams
- Department of Biochemistry, Microbiology, and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hong-Li Chou
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
11
|
Zait Y, Ferrero‐Serrano Á, Assmann SM. The α subunit of the heterotrimeric G protein regulates mesophyll CO 2 conductance and drought tolerance in rice. New Phytol 2021; 232:2324-2338. [PMID: 34515342 PMCID: PMC9293471 DOI: 10.1111/nph.17730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 09/01/2021] [Indexed: 05/03/2023]
Abstract
Mesophyll conductance gm determines CO2 diffusion rates from mesophyll intercellular air spaces to the chloroplasts and is an important factor limiting photosynthesis. Increasing gm in cultivated plants is a potential strategy to increase photosynthesis and intrinsic water use efficiency (WUEi ). The anatomy of the leaf and metabolic factors such as aquaporins and carbonic anhydrases have been identified as important determinants of gm . However, genes involved in the regulation and modulation of gm remain largely unknown. In this work, we investigated the role of heterotrimeric G proteins in gm and drought tolerance in rice d1 mutants, which harbor a null mutation in the Gα subunit gene, RGA1. d1 mutants in both cv Nipponbare and cv Taichung 65 exhibited increased gm , fostering improvement in photosynthesis, WUEi , and drought tolerance compared with wild-type. The increased surface area of mesophyll cells and chloroplasts exposed to intercellular airspaces and the reduced cell wall and chloroplast thickness in the d1 mutant are evident contributors to the increase in gm . Our results indicate that manipulation of heterotrimeric G protein signaling has the potential to improve crop WUEi and productivity under drought.
Collapse
Affiliation(s)
- Yotam Zait
- Biology DepartmentPenn State University208 Mueller LaboratoryUniversity ParkPA16802USA
| | - Ángel Ferrero‐Serrano
- Biology DepartmentPenn State University208 Mueller LaboratoryUniversity ParkPA16802USA
| | - Sarah M. Assmann
- Biology DepartmentPenn State University208 Mueller LaboratoryUniversity ParkPA16802USA
| |
Collapse
|
12
|
Gookin TE, Assmann SM. Cantil: a previously unreported organ in wild-type Arabidopsis regulated by FT, ERECTA and heterotrimeric G proteins. Development 2021; 148:269072. [PMID: 34129030 DOI: 10.1242/dev.195545] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/26/2021] [Indexed: 12/17/2022]
Abstract
We describe a previously unreported macroscopic Arabidopsis organ, the cantil, named for its 'cantilever' function of holding the pedicel at a distance from the stem. Cantil development is strongest at the first nodes after the vegetative to reproductive inflorescence transition; cantil magnitude and frequency decrease acropetally. Cantils develop in wild-type Arabidopsis accessions (e.g. Col-0, Ws and Di-G) as a consequence of delayed flowering in short days; cantil formation is observed in long days when flowering is delayed by null mutation of the floral regulator FLOWERING LOCUS T. The receptor-like kinase ERECTA is a global positive regulator of cantil formation; therefore, cantils never form in the Arabidopsis strain Ler. ERECTA functions genetically upstream of heterotrimeric G proteins. Cantil expressivity is repressed by the specific heterotrimeric complex subunits GPA1, AGB1 and AGG3, which also play independent roles: GPA1 suppresses distal spurs at cantil termini, while AGB1 and AGG3 suppress ectopic epidermal rippling. These G protein mutant traits are recapitulated in long-day flowering gpa1-3 ft-10 plants, demonstrating that cantils, spurs and ectopic rippling occur as a function of delayed phase transition, rather than as a function of photoperiod per se.
Collapse
Affiliation(s)
- Timothy E Gookin
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
13
|
Maruta N, Trusov Y, Urano D, Chakravorty D, Assmann SM, Jones AM, Botella JR. GTP binding by Arabidopsis extra-large G protein 2 is not essential for its functions. Plant Physiol 2021; 186:1240-1253. [PMID: 33729516 PMCID: PMC8195506 DOI: 10.1093/plphys/kiab119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 05/06/2023]
Abstract
The extra-large guanosine-5'-triphosphate (GTP)-binding protein 2, XLG2, is an unconventional Gα subunit of the Arabidopsis (Arabidopsis thaliana) heterotrimeric GTP-binding protein complex with a major role in plant defense. In vitro biochemical analyses and molecular dynamic simulations show that affinity of XLG2 for GTP is two orders of magnitude lower than that of the conventional Gα, AtGPA1. Here we tested the physiological relevance of GTP binding by XLG2. We generated an XLG2(T476N) variant with abolished GTP binding, as confirmed by in vitro GTPγS binding assay. Yeast three-hybrid, bimolecular fluorescence complementation, and split firefly-luciferase complementation assays revealed that the nucleotide-depleted XLG2(T476N) retained wild-type XLG2-like interactions with the Gβγ dimer and defense-related receptor-like kinases. Both wild-type and nucleotide-depleted XLG2(T476N) restored the defense responses against Fusarium oxysporum and Pseudomonas syringae compromised in the xlg2 xlg3 double mutant. Additionally, XLG2(T476N) was fully functional restoring stomatal density, root growth, and sensitivity to NaCl, but failed to complement impaired germination and vernalization-induced flowering. We conclude that XLG2 is able to function in a GTP-independent manner and discuss its possible mechanisms of action.
Collapse
Affiliation(s)
- Natsumi Maruta
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuri Trusov
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - David Chakravorty
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Alan M Jones
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
- Author for communication:
| |
Collapse
|
14
|
McFarlane HE, Mutwil-Anderwald D, Verbančič J, Picard KL, Gookin TE, Froehlich A, Chakravorty D, Trindade LM, Alonso JM, Assmann SM, Persson S. A G protein-coupled receptor-like module regulates cellulose synthase secretion from the endomembrane system in Arabidopsis. Dev Cell 2021; 56:1484-1497.e7. [PMID: 33878345 DOI: 10.1016/j.devcel.2021.03.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/16/2020] [Accepted: 03/29/2021] [Indexed: 01/18/2023]
Abstract
Cellulose is produced at the plasma membrane of plant cells by cellulose synthase (CESA) complexes (CSCs). CSCs are assembled in the endomembrane system and then trafficked to the plasma membrane. Because CESAs are only active in the plasma membrane, control of CSC secretion regulates cellulose synthesis. We identified members of a family of seven transmembrane domain-containing proteins (7TMs) that are important for cellulose production during cell wall integrity stress. 7TMs are often associated with guanine nucleotide-binding (G) protein signaling and we found that mutants affecting the Gβγ dimer phenocopied the 7tm mutants. Unexpectedly, the 7TMs localized to the Golgi/trans-Golgi network where they interacted with G protein components. Here, the 7TMs and Gβγ regulated CESA trafficking but did not affect general protein secretion. Our results outline how a G protein-coupled module regulates CESA trafficking and reveal that defects in this process lead to exacerbated responses to cell wall integrity stress.
Collapse
Affiliation(s)
- Heather E McFarlane
- School of Biosciences, University of Melbourne, Parkville 3010 VIC, Australia; Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany; Department of Cell and Systems Biology, University of Toronto, 25 Harbord St, Toronto, ON M5S 3G5, Canada.
| | - Daniela Mutwil-Anderwald
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany; School of the Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jana Verbančič
- School of Biosciences, University of Melbourne, Parkville 3010 VIC, Australia; Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - Kelsey L Picard
- School of Biosciences, University of Melbourne, Parkville 3010 VIC, Australia; School of Natural Sciences, University of Tasmania, Hobart 7001 TAS, Australia
| | - Timothy E Gookin
- Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
| | - Anja Froehlich
- Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - David Chakravorty
- Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
| | - Luisa M Trindade
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Jose M Alonso
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC 27695-7614, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA
| | - Staffan Persson
- School of Biosciences, University of Melbourne, Parkville 3010 VIC, Australia; Max-Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany; Department of Plant & Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark; Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
15
|
Zhou Y, Assmann SM, Jegla T. External Cd2+ and protons activate the hyperpolarization-gated K+ channel KAT1 at the voltage sensor. J Gen Physiol 2021; 153:211573. [PMID: 33275659 PMCID: PMC7721907 DOI: 10.1085/jgp.202012647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/21/2020] [Accepted: 11/10/2020] [Indexed: 11/20/2022] Open
Abstract
The functionally diverse cyclic nucleotide binding domain (CNBD) superfamily of cation channels contains both depolarization-gated (e.g., metazoan EAG family K+ channels) and hyperpolarization-gated channels (e.g., metazoan HCN pacemaker cation channels and the plant K+ channel KAT1). In both types of CNBD channels, the S4 transmembrane helix of the voltage sensor domain (VSD) moves outward in response to depolarization. This movement opens depolarization-gated channels and closes hyperpolarization-gated channels. External divalent cations and protons prevent or slow movement of S4 by binding to a cluster of acidic charges on the S2 and S3 transmembrane domains of the VSD and therefore inhibit activation of EAG family channels. However, a similar divalent ion/proton binding pocket has not been described for hyperpolarization-gated CNBD family channels. We examined the effects of external Cd2+ and protons on Arabidopsisthaliana KAT1 expressed in Xenopus oocytes and found that these ions strongly potentiate voltage activation. Cd2+ at 300 µM depolarizes the V50 of KAT1 by 150 mV, while acidification from pH 7.0 to 4.0 depolarizes the V50 by 49 mV. Regulation of KAT1 by Cd2+ is state dependent and consistent with Cd2+ binding to an S4-down state of the VSD. Neutralization of a conserved acidic charge in the S2 helix in KAT1 (D95N) eliminates Cd2+ and pH sensitivity. Conversely, introduction of acidic residues into KAT1 at additional S2 and S3 cluster positions that are charged in EAG family channels (N99D and Q149E in KAT1) decreases Cd2+ sensitivity and increases proton potentiation. These results suggest that KAT1, and presumably other hyperpolarization-gated plant CNBD channels, can open from an S4-down VSD conformation homologous to the divalent/proton-inhibited conformation of EAG family K+ channels.
Collapse
Affiliation(s)
- Yunqing Zhou
- Department of Biology, Penn State University, University Park, PA.,Huck Institutes of the Life Sciences, Penn State University, University Park, PA
| | - Sarah M Assmann
- Department of Biology, Penn State University, University Park, PA
| | - Timothy Jegla
- Department of Biology, Penn State University, University Park, PA.,Huck Institutes of the Life Sciences, Penn State University, University Park, PA
| |
Collapse
|
16
|
Xiang Q, Lott AA, Assmann SM, Chen S. Advances and perspectives in the metabolomics of stomatal movement and the disease triangle. Plant Sci 2021; 302:110697. [PMID: 33288010 DOI: 10.1016/j.plantsci.2020.110697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 05/20/2023]
Abstract
Crops are continuously exposed to microbial pathogens that cause tremendous yield losses worldwide. Stomatal pores formed by pairs of specialized guard cells in the leaf epidermis represent a major route of pathogen entry. Guard cells have an essential role as a first line of defense against pathogens. Metabolomics is an indispensable systems biology tool that has facilitated discovery and functional studies of metabolites that regulate stomatal movement in response to pathogens and other environmental factors. Guard cells, pathogens and environmental factors constitute the "stomatal disease triangle". The aim of this review is to highlight recent advances toward understanding the stomatal disease triangle in the context of newly discovered signaling molecules, hormone crosstalk, and consequent molecular changes that integrate pathogens and environmental sensing into stomatal immune responses. Future perspectives on emerging single-cell studies, multiomics and molecular imaging in the context of stomatal defense are discussed. Advances in this important area of plant biology will inform rational crop engineering and breeding for enhanced stomatal defense without disruption of other pathways that impact crop yield.
Collapse
Affiliation(s)
- Qingyuan Xiang
- Department of Biology, University of Florida Genetics Institute, Gainesville, FL, USA
| | - Aneirin A Lott
- Department of Biology, University of Florida Genetics Institute, Gainesville, FL, USA; Plant Molecular and Cellular Biology Program, University of Florida, FL, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, State College, PA, USA
| | - Sixue Chen
- Department of Biology, University of Florida Genetics Institute, Gainesville, FL, USA; Plant Molecular and Cellular Biology Program, University of Florida, FL, USA; Proteomics and Mass Spectrometry Facility, University of Florida, FL, USA.
| |
Collapse
|
17
|
Ritchey LE, Tack DC, Yakhnin H, Jolley EA, Assmann SM, Bevilacqua PC, Babitzke P. Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis. RNA 2020; 26:1431-1447. [PMID: 32611709 PMCID: PMC7491331 DOI: 10.1261/rna.075986.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/28/2020] [Indexed: 06/01/2023]
Abstract
RNA structure influences numerous processes in all organisms. In bacteria, these processes include transcription termination and attenuation, small RNA and protein binding, translation initiation, and mRNA stability, and can be regulated via metabolite availability and other stresses. Here we use Structure-seq2 to probe the in vivo RNA structurome of Bacillus subtilis grown in the presence and absence of amino acids. Our results reveal that amino acid starvation results in lower overall dimethyl sulfate (DMS) reactivity of the transcriptome, indicating enhanced protection owing to protein binding or RNA structure. Starvation-induced changes in DMS reactivity correlated inversely with transcript abundance changes. This correlation was particularly pronounced in genes associated with the stringent response and CodY regulons, which are involved in adaptation to nutritional stress, suggesting that RNA structure contributes to transcript abundance change in regulons involved in amino acid metabolism. Structure-seq2 accurately reported on four known amino acid-responsive riboswitches: T-box, SAM, glycine, and lysine riboswitches. Additionally, we discovered a transcription attenuation mechanism that reduces yfmG expression when amino acids are added to the growth medium. We also found that translation of a leader peptide (YfmH) encoded just upstream of yfmG regulates yfmG expression. Our results are consistent with a model in which a slow rate of yfmH translation caused by limitation of the amino acids encoded in YfmH prevents transcription termination in the yfmG leader region by favoring formation of an overlapping antiterminator structure. This novel RNA switch offers a way to simultaneously monitor the levels of multiple amino acids.
Collapse
Affiliation(s)
- Laura E Ritchey
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David C Tack
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elizabeth A Jolley
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
18
|
Maheshwari P, Assmann SM, Albert R. A Guard Cell Abscisic Acid (ABA) Network Model That Captures the Stomatal Resting State. Front Physiol 2020; 11:927. [PMID: 32903539 PMCID: PMC7438572 DOI: 10.3389/fphys.2020.00927] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
Stomatal pores play a central role in the control of carbon assimilation and plant water status. The guard cell pair that borders each pore integrates information from environmental and endogenous signals and accordingly swells or deflates, thereby increasing or decreasing the stomatal aperture. Prior research shows that there is a complex cellular network underlying this process. We have previously constructed a signal transduction network and a Boolean dynamic model describing stomatal closure in response to signals including the plant hormone abscisic acid (ABA), calcium or reactive oxygen species (ROS). Here, we improve the Boolean network model such that it captures the biologically expected response of the guard cell in the absence or following the removal of a closure-inducing signal such as ABA or external Ca2+. The expectation from the biological system is reversibility, i.e., the stomata should reopen after the closing signal is removed. We find that the model's reversibility is obstructed by the previously assumed persistent activity of four nodes. By introducing time-dependent Boolean functions for these nodes, the model recapitulates stomatal reopening following the removal of a signal. The previous version of the model predicts ∼20% closure in the absence of any signal due to uncertainty regarding the initial conditions of multiple network nodes. We systematically test and adjust these initial conditions to find the minimally restrictive combinations that appropriately result in open stomata in the absence of a closure signal. We support these results by an analysis of the successive stabilization of feedback motifs in the network, illuminating the system's dynamic progression toward the open or closed stomata state. This analysis particularly highlights the role of cytosolic calcium oscillations in causing and maintaining stomatal closure. Overall, we illustrate the strength of the Boolean network modeling framework to efficiently capture cellular phenotypes as emergent outcomes of intracellular biological processes.
Collapse
Affiliation(s)
- Parul Maheshwari
- Department of Physics, Penn State University, University Park, PA, United States
| | - Sarah M Assmann
- Department of Biology, Penn State University, University Park, PA, United States
| | - Reka Albert
- Department of Physics, Penn State University, University Park, PA, United States.,Department of Biology, Penn State University, University Park, PA, United States
| |
Collapse
|
19
|
Kong W, Yoo MJ, Zhu D, Noble JD, Kelley TM, Li J, Kirst M, Assmann SM, Chen S. Molecular changes in Mesembryanthemum crystallinum guard cells underlying the C 3 to CAM transition. Plant Mol Biol 2020; 103:653-667. [PMID: 32468353 DOI: 10.1007/s11103-020-01016-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 05/17/2020] [Indexed: 05/14/2023]
Abstract
KEY MESSAGE: The timing and transcriptomic changes during the C3 to CAM transition of common ice plant support the notion that guard cells themselves can shift from C3 to CAM. Crassulacean acid metabolism (CAM) is a specialized type of photosynthesis: stomata close during the day, enhancing water conservation, and open at night, allowing CO2 uptake. Mesembryanthemum crystallinum (common ice plant) is a facultative CAM species that can shift from C3 photosynthesis to CAM under salt or drought stresses. However, the molecular mechanisms underlying the stress induced transition from C3 to CAM remain unknown. Here we determined the transition time from C3 to CAM in M. crystallinum under salt stress. In parallel, single-cell-type transcriptomic profiling by 3'-mRNA sequencing was conducted in isolated stomatal guard cells to determine the molecular changes in this key cell type during the transition. In total, 495 transcripts showed differential expression between control and salt-treated samples during the transition, including 285 known guard cell genes, seven CAM-related genes, 18 transcription factors, and 185 other genes previously not found to be expressed in guard cells. PEPC1 and PPCK1, which encode key enzymes of CAM photosynthesis, were up-regulated in guard cells after seven days of salt treatment, indicating that guard cells themselves can shift from C3 to CAM. This study provides important information towards introducing CAM stomatal behavior into C3 crops to enhance water use efficiency.
Collapse
Affiliation(s)
- Wenwen Kong
- College of Life Sciences, Northeast Agricultural University, Harbin, China
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
- Guangdong Province Key Laboratory for Plant Epigenetics, College of Life Science and Oceanography, Shenzhen University, Shenzhen, China
| | - Mi-Jeong Yoo
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
| | - Dan Zhu
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
- College of Life Science, Key Lab of Plant Biotechnology in Universities of Shandong Province, Qingdao Agricultural University, Qingdao, China
| | - Jerald D Noble
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA
| | - Theresa M Kelley
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA
| | - Jing Li
- College of Life Sciences, Northeast Agricultural University, Harbin, China
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, USA.
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, USA.
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida (UF), Gainesville, FL, USA.
| |
Collapse
|
20
|
Tack DC, Su Z, Yu Y, Bevilacqua PC, Assmann SM. Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis. RNA 2020; 26:492-511. [PMID: 31937672 PMCID: PMC7075263 DOI: 10.1261/rna.072850.119] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/13/2020] [Indexed: 05/22/2023]
Abstract
Little is known concerning the effects of abiotic factors on in vivo RNA structures. We applied Structure-seq to assess the in vivo mRNA structuromes of Arabidopsis thaliana under salinity stress, which negatively impacts agriculture. Structure-seq utilizes dimethyl sulfate reactivity to identify As and Cs that lack base-pairing or protection. Salt stress refolded transcripts differentially in root versus shoot, evincing tissue specificity of the structurome. Both tissues exhibited an inverse correlation between salt stress-induced changes in transcript reactivity and changes in abundance, with stress-related mRNAs showing particular structural dynamism. This inverse correlation is more pronounced in mRNAs wherein the mean reactivity of the 5'UTR, CDS, and 3'UTR concertedly change under salinity stress, suggesting increased susceptibility to abundance control mechanisms in transcripts exhibiting this phenomenon, which we name "concordancy." Concordant salinity-induced increases in reactivity were notably observed in photosynthesis genes, thereby implicating mRNA structural loss in the well-known depression of photosynthesis by salt stress. Overall, changes in secondary structure appear to impact mRNA abundance, molding the functional specificity of the transcriptome under stress.
Collapse
Affiliation(s)
- David C Tack
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Spectrum Health Office of Research, Grand Rapids, Michigan 49503, USA
| | - Zhao Su
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Yunqing Yu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
21
|
Zhu M, Geng S, Chakravorty D, Guan Q, Chen S, Assmann SM. Metabolomics of red-light-induced stomatal opening in Arabidopsis thaliana: Coupling with abscisic acid and jasmonic acid metabolism. Plant J 2020; 101:1331-1348. [PMID: 31677315 DOI: 10.1111/tpj.14594] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 09/20/2019] [Accepted: 09/30/2019] [Indexed: 06/10/2023]
Abstract
Environmental stimuli-triggered stomatal movement is a key physiological process that regulates CO2 uptake and water loss in plants. Stomata are defined by pairs of guard cells that perceive and transduce external signals, leading to cellular volume changes and consequent stomatal aperture change. Within the visible light spectrum, red light induces stomatal opening in intact leaves. However, there has been debate regarding the extent to which red-light-induced stomatal opening arises from direct guard cell sensing of red light versus indirect responses as a result of red light influences on mesophyll photosynthesis. Here we identify conditions that result in red-light-stimulated stomatal opening in isolated epidermal peels and enlargement of protoplasts, firmly establishing a direct guard cell response to red light. We then employ metabolomics workflows utilizing gas chromatography mass spectrometry and liquid chromatography mass spectrometry for metabolite profiling and identification of Arabidopsis guard cell metabolic signatures in response to red light in the absence of the mesophyll. We quantified 223 metabolites in Arabidopsis guard cells, with 104 found to be red light responsive. These red-light-modulated metabolites participate in the tricarboxylic acid cycle, carbon balance, phytohormone biosynthesis and redox homeostasis. We next analyzed selected Arabidopsis mutants, and discovered that stomatal opening response to red light is correlated with a decrease in guard cell abscisic acid content and an increase in jasmonic acid content. The red-light-modulated guard cell metabolome reported here provides fundamental information concerning autonomous red light signaling pathways in guard cells.
Collapse
Affiliation(s)
- Mengmeng Zhu
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sisi Geng
- The Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
| | - David Chakravorty
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Qijie Guan
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Sixue Chen
- The Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
22
|
Zhou Y, Assmann SM, Jegla TJ. Cadmium and Protons Activate the Plant Hyperpolarization-gated K+ Channel KAT1 through a Conserved Binding Site in the Voltage Sensor Domain. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
23
|
Waldron JA, Tack DC, Ritchey LE, Gillen SL, Wilczynska A, Turro E, Bevilacqua PC, Assmann SM, Bushell M, Le Quesne J. mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity. Genome Biol 2019; 20:300. [PMID: 31888698 PMCID: PMC6936103 DOI: 10.1186/s13059-019-1901-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The RNA helicase eIF4A1 is a key component of the translation initiation machinery and is required for the translation of many pro-oncogenic mRNAs. There is increasing interest in targeting eIF4A1 therapeutically in cancer, thus understanding how this protein leads to the selective re-programming of the translational landscape is critical. While it is known that eIF4A1-dependent mRNAs frequently have long GC-rich 5'UTRs, the details of how 5'UTR structure is resculptured by eIF4A1 to enhance the translation of specific mRNAs are unknown. RESULTS Using Structure-seq2 and polysome profiling, we assess global mRNA structure and translational efficiency in MCF7 cells, with and without eIF4A inhibition with hippuristanol. We find that eIF4A inhibition does not lead to global increases in 5'UTR structure, but rather it leads to 5'UTR remodeling, with localized gains and losses of structure. The degree of these localized structural changes is associated with 5'UTR length, meaning that eIF4A-dependent mRNAs have greater localized gains of structure due to their increased 5'UTR length. However, it is not solely increased localized structure that causes eIF4A-dependency but the position of the structured regions, as these structured elements are located predominantly at the 3' end of the 5'UTR. CONCLUSIONS By measuring changes in RNA structure following eIF4A inhibition, we show that eIF4A remodels local 5'UTR structures. The location of these structural elements ultimately determines the dependency on eIF4A, with increased structure just upstream of the CDS being the major limiting factor in translation, which is overcome by eIF4A activity.
Collapse
Affiliation(s)
- Joseph A Waldron
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
| | - David C Tack
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Present Address: Spectrum Health Office of Research, 100 Michigan Street NE, Mail Code 038, Grand Rapids, MI, 49503, USA
| | - Laura E Ritchey
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Present Address: Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, PA, 15904, USA
| | - Sarah L Gillen
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Ania Wilczynska
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge, UK
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge, UK
- National Institute for Health Research BioResource, Cambridge University Hospitals, Cambridge, UK
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK.
| | - John Le Quesne
- Medical Research Council Toxicology Unit, University of Cambridge, Hodgkin Building, Lancaster Road, Leicester, LE1 7HB, UK.
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK.
| |
Collapse
|
24
|
Maruta N, Trusov Y, Chakravorty D, Urano D, Assmann SM, Botella JR. Nucleotide exchange-dependent and nucleotide exchange-independent functions of plant heterotrimeric GTP-binding proteins. Sci Signal 2019; 12:12/606/eaav9526. [PMID: 31690635 DOI: 10.1126/scisignal.aav9526] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins), which are composed of α, β, and γ subunits, are versatile, guanine nucleotide-dependent, molecular on-off switches. In animals and fungi, the exchange of GDP for GTP on Gα controls G protein activation and is crucial for normal cellular responses to diverse extracellular signals. The model plant Arabidopsis thaliana has a single canonical Gα subunit, AtGPA1. We found that, in planta, the constitutively active, GTP-bound AtGPA1(Q222L) mutant and the nucleotide-free AtGPA1(S52C) mutant interacted with Gβγ1 and Gβγ2 dimers with similar affinities, suggesting that G protein heterotrimer formation occurred independently of nucleotide exchange. In contrast, AtGPA1(Q222L) had a greater affinity than that of AtGPA1(S52C) for Gβγ3, suggesting that the GTP-bound conformation of AtGPA1(Q222L) is distinct and tightly associated with Gβγ3. Functional analysis of transgenic lines expressing either AtGPA1(S52C) or AtGPA1(Q222L) in the gpa1-null mutant background revealed various mutant phenotypes that were complemented by either AtGPA1(S52C) or AtGPA1(Q222L). We conclude that, in addition to the canonical GDP-GTP exchange-dependent mechanism, plant G proteins can function independently of nucleotide exchange.
Collapse
Affiliation(s)
- Natsumi Maruta
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yuri Trusov
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - David Chakravorty
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Daisuke Urano
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Jose R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia. .,State Key Laboratory of Cotton Biology, Department of Biology, Institute of Plant Stress Biology, Henan University, Kaifeng 475001, China
| |
Collapse
|
25
|
Abstract
Semidwarf stature is a valuable agronomic trait in grain crops that reduces lodging and increases harvest index. A fundamental advance during the 1960s Green Revolution was the introduction of semidwarf cultivars of rice and wheat. Essentially, all semidwarf varieties of rice under cultivation today owe their diminished stature to a specific null mutation in the gibberellic acid (GA) biosynthesis gene, SD1 However, it is now well-established that, in addition to GAs, brassinosteroids and strigolactones also control plant height. In this review, we describe the synthesis and signaling pathways of these three hormones as understood in rice and discuss the mutants and transgenics in these pathways that confer semidwarfism and other valuable architectural traits. We propose that such genes offer underexploited opportunities for broadening the genetic basis and germplasm in semidwarf rice breeding.
Collapse
Affiliation(s)
| | - Christian Cantos
- Biology Department, Penn State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
26
|
Maheshwari P, Du H, Sheen J, Assmann SM, Albert R. Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling. PLoS Comput Biol 2019; 15:e1007429. [PMID: 31658257 PMCID: PMC6837631 DOI: 10.1371/journal.pcbi.1007429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 11/07/2019] [Accepted: 09/21/2019] [Indexed: 11/19/2022] Open
Abstract
The plant hormone abscisic acid (ABA) promotes stomatal closure via multifarious cellular signaling cascades. Our previous comprehensive reconstruction of the stomatal closure network resulted in an 81-node network with 153 edges. Discrete dynamic modeling utilizing this network reproduced over 75% of experimental observations but a few experimentally supported results were not recapitulated. Here we identify predictions that improve the agreement between model and experiment. We performed dynamics-preserving network reduction, resulting in a condensed 49 node and 113 edge stomatal closure network that preserved all dynamics-determining network motifs and reproduced the predictions of the original model. We then utilized the reduced network to explore cases in which experimental activation of internal nodes in the absence of ABA elicited stomatal closure in wet bench experiments, but not in our in silico model. Our simulations revealed that addition of a single edge, which allows indirect inhibition of any one of three PP2C protein phosphatases (ABI2, PP2CA, HAB1) by cytosolic Ca2+ elevation, resolves the majority of the discrepancies. Consistent with this hypothesis, we experimentally show that Ca2+ application to cellular lysates at physiological concentrations inhibits PP2C activity. The model augmented with this new edge provides new insights into the role of cytosolic Ca2+ oscillations in stomatal closure, revealing a mutual reinforcement between repeated increases in cytosolic Ca2+ concentration and a self-sustaining feedback circuit inside the signaling network. These results illustrate how iteration between model and experiment can improve predictions of highly complex cellular dynamics.
Collapse
Affiliation(s)
- Parul Maheshwari
- Department of Physics, Penn State University, University Park, Pennsylvania, United States of America
| | - Hao Du
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sarah M. Assmann
- Biology Department, Penn State University, University Park, Pennsylvania, United States of America
| | - Reka Albert
- Department of Physics, Penn State University, University Park, Pennsylvania, United States of America
- Biology Department, Penn State University, University Park, Pennsylvania, United States of America
| |
Collapse
|
27
|
Mitchell D, Assmann SM, Bevilacqua PC. Probing RNA structure in vivo. Curr Opin Struct Biol 2019; 59:151-158. [PMID: 31521910 DOI: 10.1016/j.sbi.2019.07.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 01/30/2023]
Abstract
RNA structure underpins many essential functions in biology. New chemical reagents and techniques for probing RNA structure in living cells have emerged in recent years. High-throughput, genome-wide techniques such as Structure-seq2 and DMS-MaPseq exploit nucleobase modification by dimethylsulfate (DMS) to obtain complete structuromes, and are applicable to multiple domains of life and conditions. New reagents such as 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC), glyoxal, and nicotinoyl azide (NAz) greatly expand the capabilities of nucleobase probing in cells. Additionally, ribose-targeting reagents in selective 2'-hydroxyl acylation and primer extension (SHAPE) detect RNA flexibility in vivo. These techniques, coupled with crosslinking nucleobases in psoralen analysis of RNA interactions and structures (PARIS), provide new and diverse ways to elucidate RNA secondary and tertiary structure in vivo and genome-wide.
Collapse
Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Sarah M Assmann
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
28
|
Spasic A, Assmann SM, Bevilacqua PC, Mathews DH. Modeling RNA secondary structure folding ensembles using SHAPE mapping data. Nucleic Acids Res 2019; 46:314-323. [PMID: 29177466 PMCID: PMC5758915 DOI: 10.1093/nar/gkx1057] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 10/30/2017] [Indexed: 12/22/2022] Open
Abstract
RNA secondary structure prediction is widely used for developing hypotheses about the structures of RNA sequences, and structure can provide insight about RNA function. The accuracy of structure prediction is known to be improved using experimental mapping data that provide information about the pairing status of single nucleotides, and these data can now be acquired for whole transcriptomes using high-throughput sequencing. Prior methods for using these experimental data focused on predicting structures for sequences assuming that they populate a single structure. Most RNAs populate multiple structures, however, where the ensemble of strands populates structures with different sets of canonical base pairs. The focus on modeling single structures has been a bottleneck for accurately modeling RNA structure. In this work, we introduce Rsample, an algorithm for using experimental data to predict more than one RNA structure for sequences that populate multiple structures at equilibrium. We demonstrate, using SHAPE mapping data, that we can accurately model RNA sequences that populate multiple structures, including the relative probabilities of those structures. This program is freely available as part of the RNAstructure software package.
Collapse
Affiliation(s)
- Aleksandar Spasic
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Department of Biochemistry & Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biostatistics & Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| |
Collapse
|
29
|
Jeon BW, Acharya BR, Assmann SM. The Arabidopsis heterotrimeric G-protein β subunit, AGB1, is required for guard cell calcium sensing and calcium-induced calcium release. Plant J 2019; 99:231-244. [PMID: 30882980 DOI: 10.1111/tpj.14318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/04/2019] [Accepted: 03/13/2019] [Indexed: 05/08/2023]
Abstract
Cytosolic calcium concentration ([Ca2+ ]cyt ) and heterotrimeric G-proteins are universal eukaryotic signaling elements. In plant guard cells, extracellular calcium (Cao ) is as strong a stimulus for stomatal closure as the phytohormone abscisic acid (ABA), but underlying mechanisms remain elusive. Here, we report that the sole Arabidopsis heterotrimeric Gβ subunit, AGB1, is required for four guard cell Cao responses: induction of stomatal closure; inhibition of stomatal opening; [Ca2+ ]cyt oscillation; and inositol 1,4,5-trisphosphate (InsP3) production. Stomata in wild-type Arabidopsis (Col) and in mutants of the canonical Gα subunit, GPA1, showed inhibition of stomatal opening and promotion of stomatal closure by Cao . By contrast, stomatal movements of agb1 mutants and agb1/gpa1 double-mutants, as well as those of the agg1agg2 Gγ double-mutant, were insensitive to Cao . These behaviors contrast with ABA-regulated stomatal movements, which involve GPA1 and AGB1/AGG3 dimers, illustrating differential partitioning of G-protein subunits among stimuli with similar ultimate impacts, which may facilitate stimulus-specific encoding. AGB1 knockouts retained reactive oxygen species and NO production, but lost YC3.6-detected [Ca2+ ]cyt oscillations in response to Cao , initiating only a single [Ca2+ ]cyt spike. Experimentally imposed [Ca2+ ]cyt oscillations restored stomatal closure in agb1. Yeast two-hybrid and bimolecular complementation fluorescence experiments revealed that AGB1 interacts with phospholipase Cs (PLCs), and Cao induced InsP3 production in Col but not in agb1. In sum, G-protein signaling via AGB1/AGG1/AGG2 is essential for Cao -regulation of stomatal apertures, and stomatal movements in response to Cao apparently require Ca2+ -induced Ca2+ release that is likely dependent on Gβγ interaction with PLCs leading to InsP3 production.
Collapse
Affiliation(s)
- Byeong Wook Jeon
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju, 61186, Korea
| | - Biswa R Acharya
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
30
|
Argueso CT, Assmann SM, Birnbaum KD, Chen S, Dinneny JR, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall‐Colón A, Mason GA, O'Lexy R, Peck SC, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM. Directions for research and training in plant omics: Big Questions and Big Data. Plant Direct 2019; 3:e00133. [PMID: 31245771 PMCID: PMC6589541 DOI: 10.1002/pld3.133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/21/2019] [Indexed: 05/04/2023]
Abstract
A key remit of the NSF-funded "Arabidopsis Research and Training for the 21st Century" (ART-21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research using Arabidopsis thaliana can play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al., Plant Physiology, 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the second ART-21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post-doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.
Collapse
Affiliation(s)
- Cristiana T. Argueso
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsColorado
| | - Sarah M. Assmann
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvania
| | - Kenneth D. Birnbaum
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNew York
| | - Sixue Chen
- Department of BiologyGenetics InstitutePlant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida
- Proteomics and Mass SpectrometryInterdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFlorida
| | | | - Colleen J. Doherty
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth Carolina
| | | | | | - Vanessa R. Greenlee
- International ProgramsCollege of Agriculture and Life SciencesCornell UniversityIthacaNew York
| | - Julie A. Law
- Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCalifornia
- Division of Biological SciencesUniversity of California, San DiegoLa JollaCalifornia
| | - Amy Marshall‐Colón
- Department of Plant BiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinois
| | - Grace Alex Mason
- Department of Plant Biology and Genome CenterUC DavisDavisCalifornia
| | - Ruby O'Lexy
- Coriell Institute for Medical ResearchCamdenNew Jersey
| | - Scott C. Peck
- Division of BiochemistryChristopher S. Bond Life Sciences CenterInterdisciplinary Plant GroupUniversity of MissouriColumbiaMissouri
| | | | - Liang Song
- Department of BotanyThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | | | | | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowa
| | - Cranos M. Williams
- Department of Electrical and Computer EngineeringNorth Carolina State UniversityRaleighNorth Carolina
| |
Collapse
|
31
|
Mitchell D, Renda AJ, Douds CA, Babitzke P, Assmann SM, Bevilacqua PC. In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). RNA 2019; 25:147-157. [PMID: 30341176 PMCID: PMC6298566 DOI: 10.1261/rna.067868.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/18/2018] [Indexed: 05/09/2023]
Abstract
Many biological functions performed by RNAs arise from their in vivo structures. The structure of the same RNA can differ in vitro and in vivo owing in part to the influence of molecules ranging from protons to secondary metabolites to proteins. Chemical reagents that modify the Watson-Crick (WC) face of unprotected RNA bases report on the absence of base-pairing and so are of value to determining structures adopted by RNAs. Reagents have thus been sought that can report on the native RNA structures that prevail in living cells. Dimethyl sulfate (DMS) and glyoxal penetrate cell membranes and inform on RNA secondary structure in vivo through modification of adenine (A), cytosine (C), and guanine (G) bases. Uracil (U) bases, however, have thus far eluded characterization in vivo. Herein, we show that the water-soluble carbodiimide 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is capable of modifying the WC face of U and G in vivo, favoring the former nucleobase by a factor of ∼1.5, and doing so in the eukaryote rice, as well as in the Gram-negative bacterium Escherichia coli While both EDC and glyoxal target Gs, EDC reacts with Gs in their typical neutral state, while glyoxal requires Gs to populate the rare anionic state. EDC may thus be more generally useful; however, comparison of the reactivity of EDC and glyoxal may allow the identification of Gs with perturbed pKas in vivo and genome-wide. Overall, use of EDC with DMS allows in vivo probing of the base-pairing status of all four RNA bases.
Collapse
MESH Headings
- Base Pairing
- Base Sequence
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Ethyldimethylaminopropyl Carbodiimide
- Glyoxal
- Guanine/chemistry
- Indicators and Reagents
- Molecular Probe Techniques
- Molecular Probes
- Molecular Structure
- Nucleic Acid Conformation
- Oryza/chemistry
- Oryza/genetics
- RNA/chemistry
- RNA/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Uracil/chemistry
Collapse
Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew J Renda
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Catherine A Douds
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
32
|
Abstract
In vivo genome-wide RNA structure probing provides a global view of RNA structure as it occurs in the cell and can assist in elucidating important functional aspects of RNA structure. Structure-seq2 provides high-quality data on transcriptome-wide RNA structure in vivo but contains numerous steps that require technical precision. In this chapter we present the steps needed to produce high-quality structural data with a focus on controls and troubleshooting. Structure-seq2 can be applied to numerous organisms including plants, humans, and bacteria and is amenable to a wide variety of RNA-modifying chemicals including DMS, glyoxal, and SHAPE reagents. Notably, the data generated by the method highlighted here can be readily analyzed using our StructureFold2 computational pipeline.
Collapse
Affiliation(s)
- Laura E Ritchey
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Chemistry, University of Pittsburgh at Johnstown, Johnstown, PA, USA
| | - Zhao Su
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Sarah M Assmann
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA.
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA.
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA.
| |
Collapse
|
33
|
Jegla T, Busey G, Assmann SM. Evolution and Structural Characteristics of Plant Voltage-Gated K + Channels. Plant Cell 2018; 30:2898-2909. [PMID: 30389753 PMCID: PMC6354262 DOI: 10.1105/tpc.18.00523] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/09/2018] [Accepted: 10/30/2018] [Indexed: 05/18/2023]
Abstract
Plant voltage-gated K+ channels have been referred to as "plant Shakers" in reference to animal Shaker channels, the first K+ channels identified. Recent advances in our knowledge of K+ channel evolution and structure have significantly deepened the divide between these plant and animal K+ channels, suggesting that it is time to completely retire the "plant Shaker" designation. Evolutionary genomics reveals that plant voltage-gated K+ channels and metazoan Shakers derive from distinct prokaryotic ancestors. The plant channels belong to a lineage that includes cyclic nucleotide-gated channels and metazoan ether-à-go-go and hyperpolarization-activated, cyclic nucleotide-gated channels. We refer to this lineage as the CNBD channel superfamily, because all these channels share a cytoplasmic gating domain homologous to cyclic nucleotide binding domains. The first structures of CNBD superfamily channels reveal marked differences in coupling between the voltage sensor and ion-conducting pore relative to metazoan Shaker channels. Viewing plant voltage-gated K+ channel function through the lens of CNBD superfamily structures should lead to insights into how these channels are regulated.
Collapse
Affiliation(s)
- Timothy Jegla
- Department of Biology and Huck Institute for the Life Sciences, Penn State University, 230 Life Sciences Building, University Park, Pennsylvania 16802
| | - Gregory Busey
- Department of Biology, Penn State University, 225 Life Sciences Building, University Park, Pennsylvania 16802
| | - Sarah M Assmann
- Department of Biology, Penn State University, 354 North Frear, University Park, Pennsylvania 16802
| |
Collapse
|
34
|
Abstract
How organisms perceive and respond to their surroundings is one of the great questions in biology. It is clear that RNA plays key roles in sensing. Cellular and environmental cues that RNA responds to include temperature, ions, metabolites, and biopolymers. Recent advances in next-generation sequencing and in vivo chemical probing have provided unprecedented insights into RNA folding in vivo and genome-wide. Patterns of chemical reactivity have implicated control of gene expression by RNA and aided prediction of RNA structure. Central to these advances has been development of molecular biological and chemical techniques. Key advances are improvements in the quality, cost, and throughput of library preparation; availability of a wider array of chemicals for probing RNA structure in vivo; and robustness and user friendliness of data analysis. Insights from probing transcriptomes and future directions are provided.
Collapse
Affiliation(s)
- Philip C Bevilacqua
- Departments of Chemistry and Biochemistry & Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| |
Collapse
|
35
|
Yu Y, Assmann SM. Inter-relationships between the heterotrimeric Gβ subunit AGB1, the receptor-like kinase FERONIA, and RALF1 in salinity response. Plant Cell Environ 2018; 41:2475-2489. [PMID: 29907954 PMCID: PMC6150805 DOI: 10.1111/pce.13370] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 05/06/2023]
Abstract
Plant heterotrimeric G proteins modulate numerous developmental stress responses. Recently, receptor-like kinases (RLKs) have been implicated as functioning with G proteins and may serve as plant G-protein-coupled-receptors. The RLK FERONIA (FER), in the Catharantus roseus RLK1-like subfamily, is activated by a family of polypeptides called rapid alkalinization factors (RALFs). We previously showed that the Arabidopsis G protein β subunit, AGB1, physically interacts with FER, and that RALF1 regulation of stomatal movement through FER requires AGB1. Here, we investigated genetic interactions of AGB1 and FER in plant salinity response by comparing salt responses in the single and double mutants of agb1 and fer. We show that AGB1 and FER act additively or synergistically depending on the conditions of the NaCl treatments. We further show that the synergism likely occurs through salt-induced ROS production. In addition, we show that RALF1 enhances salt toxicity through increasing Na+ accumulation and decreasing K+ accumulation rather than by inducing ROS production, and that the RALF1 effect on salt response occurs in an AGB1-independent manner. Our results indicate that RLK epistatic relationships are not fixed, as AGB1 and FER display different genetic relationships to RALF1 in stomatal versus salinity responses.
Collapse
Affiliation(s)
| | - Sarah M. Assmann
- To whom correspondence should be addressed: , tel. 814-863-9579, fax. 814-865-9131
| |
Collapse
|
36
|
Chakravorty D, Yu Y, Assmann SM. A kinase-dead version of FERONIA receptor-like kinase has dose-dependent impacts on rosette morphology and RALF1-mediated stomatal movements. FEBS Lett 2018; 592:3429-3437. [PMID: 30207378 PMCID: PMC6205910 DOI: 10.1002/1873-3468.13249] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 12/18/2022]
Abstract
The receptor-like kinase FERONIA (FER) pleiotropically affects plant reproduction, development, and stress tolerance. We recently showed that the FER ligand RALF1 promotes stomatal closure and inhibits stomatal opening in a G-protein-dependent manner. FER responses have been designated as kinase-dependent or kinase-independent, based largely on fer complementation assays employing a kinase-dead FERK565R. Our quantification of FERK565R-GFP transcript and FERK565R-GFP protein in fer complementation lines reveal that, even within individual complementation lines, different levels of FERK565R expression prevail. FERK565R-GFP expression comparable to that of FER in Col-0 plants fail to elicit complementation of either fer rosette phenotypes or RALF1-elicited stomatal movements, whereas overexpression levels of FERK565R-GFP result in complementation. These results suggest possible alternative interpretations of previous conclusions regarding kinase-independent FER signaling.
Collapse
Affiliation(s)
- David Chakravorty
- Biology Department, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA, USA
| | - Yunqing Yu
- Biology Department, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA, USA
| | - Sarah M Assmann
- Biology Department, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
37
|
Yu Y, Chakravorty D, Assmann SM. The G Protein β-Subunit, AGB1, Interacts with FERONIA in RALF1-Regulated Stomatal Movement. Plant Physiol 2018; 176:2426-2440. [PMID: 29301953 PMCID: PMC5841690 DOI: 10.1104/pp.17.01277] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/03/2018] [Indexed: 05/04/2023]
Abstract
Heterotrimeric guanine nucleotide-binding (G) proteins are composed of Gα, Gβ, and Gγ subunits and function as molecular switches in signal transduction. In Arabidopsis (Arabidopsis thaliana), there are one canonical Gα (GPA1), three extra-large Gα (XLG1, XLG2, and XLG3), one Gβ (AGB1), and three Gγ (AGG1, AGG2, and AGG3) subunits. To elucidate AGB1 molecular signaling, we performed immunoprecipitation using plasma membrane-enriched proteins followed by mass spectrometry to identify the protein interactors of AGB1. After eliminating proteins present in the control immunoprecipitation, commonly identified contaminants, and organellar proteins, a total of 103 candidate AGB1-associated proteins were confidently identified. We identified all of the G protein subunits except XLG1, receptor-like kinases, Ca2+ signaling-related proteins, and 14-3-3-like proteins, all of which may couple with or modulate G protein signaling. We confirmed physical interaction between AGB1 and the receptor-like kinase FERONIA (FER) using bimolecular fluorescence complementation. The Rapid Alkalinization Factor (RALF) family of polypeptides have been shown to be ligands of FER. In this study, we demonstrate that RALF1 regulates stomatal apertures and does so in a G protein-dependent manner, inhibiting stomatal opening and promoting stomatal closure in Columbia but not in agb1 mutants. We further show that AGGs and XLGs, but not GPA1, participate in RALF1-mediated stomatal signaling. Our results suggest that FER acts as a G protein-coupled receptor for plant heterotrimeric G proteins.
Collapse
Affiliation(s)
- Yunqing Yu
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - David Chakravorty
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, University Park, Pennsylvania 16802
| |
Collapse
|
38
|
Tack DC, Tang Y, Ritchey LE, Assmann SM, Bevilacqua PC. StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis. Methods 2018; 143:12-15. [PMID: 29410279 DOI: 10.1016/j.ymeth.2018.01.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/12/2018] [Accepted: 01/29/2018] [Indexed: 11/17/2022] Open
Abstract
The secondary structure of an RNA is often implicit to its function. Recently, various high-throughput RNA structure probing techniques have been developed to elucidate important RNA structure-function relationships genome-wide. These techniques produce unwieldy experimental data sets that require evaluation with unique computational pipelines. Herein, we present StructureFold2, a user-friendly set of analysis tools that makes precise data processing and detailed downstream analyses of such data sets both available and practical. StructureFold2 processes high-throughput reads sequenced from libraries prepared after experimental probing for reverse transcription (RT) stops generated by chemical modification of RNA at solvent accessible residues. This pipeline is able to analyze reads generated from a variety of structure-probing chemicals (e.g. DMS, glyoxal, SHAPE). Notably, StructureFold2 offers a new fully featured suite of utilities and tools to guide a user through multiple types of analyses. A particular emphasis is placed on analyzing the reactivity patterns of transcripts, complementing their use as folding restraints for predicting RNA secondary structure. StructureFold2 is hosted as a Github repository and is available at (https://github.com/StructureFold2/StructureFold2).
Collapse
Affiliation(s)
- David C Tack
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
| | - Yin Tang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Laura E Ritchey
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
39
|
Ferrero-Serrano Á, Su Z, Assmann SM. Illuminating the role of the Gα heterotrimeric G protein subunit, RGA1, in regulating photoprotection and photoavoidance in rice. Plant Cell Environ 2018; 41:451-468. [PMID: 29216416 DOI: 10.1111/pce.13113] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 05/22/2023]
Abstract
We studied physiological mechanisms of photoavoidance and photoprotection of a dwarf rice mutant with erect leaves, d1, in which the RGA1 gene, which encodes the Gα subunit of the heterotrimeric G protein, is non-functional. Leaves of d1 exhibit lower leaf temperature and higher photochemical reflectance index relative to wild type (WT), indicative of increased photoavoidance and more efficient light harvesting. RNA sequencing analysis of flag leaves revealed that messenger RNA levels of genes encoding heat shock proteins, enzymes associated with chlorophyll breakdown, and ROS scavengers were down-regulated in d1. By contrast, genes encoding proteins associated with light harvesting, Photosystem II, cyclic electron transport, Photosystem I, and chlorophyll biosynthesis were up-regulated in d1. Consistent with these observations, when WT and d1 plants were experimentally subjected to the same light intensity, d1 plants exhibited a greater capacity to dissipate excess irradiance (increased nonphotochemical quenching) relative to WT. The increased capacity in d1 for both photoavoidance and photoprotection reduced sustained photoinhibitory damage, as revealed by a higher Fv /Fm . We therefore propose RGA1 as a regulator of photoavoidance and photoprotection mechanisms in rice and highlight the prospect of exploiting modulation of heterotrimeric G protein signalling to increase these characteristics and improve the yield of cereals in the event of abiotic stress.
Collapse
Affiliation(s)
- Ángel Ferrero-Serrano
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Zhao Su
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| |
Collapse
|
40
|
Mitchell D, Ritchey LE, Park H, Babitzke P, Assmann SM, Bevilacqua PC. Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA 2018; 24:114-124. [PMID: 29030489 PMCID: PMC5733565 DOI: 10.1261/rna.064014.117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 10/10/2017] [Indexed: 05/09/2023]
Abstract
Elucidation of the folded structures that RNA forms in vivo is vital to understanding its functions. Chemical reagents that modify the Watson-Crick (WC) face of unprotected nucleobases are particularly useful in structure elucidation. Dimethyl sulfate penetrates cell membranes and informs on RNA base-pairing and secondary structure but only modifies the WC face of adenines and cytosines. We present glyoxal, methylglyoxal, and phenylglyoxal as potent in vivo reagents that target the WC face of guanines as well as cytosines and adenines. Tests on rice (Oryza sativa) 5.8S rRNA in vitro read out by reverse transcription and gel electrophoresis demonstrate specific modification of almost all guanines in a time- and pH-dependent manner. Subsequent in vivo tests on rice, a eukaryote, and Bacillus subtilis and Escherichia coli, Gram-positive and Gram-negative bacteria, respectively, showed that all three reagents enter living cells without prior membrane permeabilization or pH adjustment of the surrounding media and specifically modify solvent-exposed guanine, cytosine, and adenine residues.
Collapse
Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Laura E Ritchey
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hongmarn Park
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
41
|
Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM. The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology. Plant Physiol 2017; 175:1499-1509. [PMID: 29208732 PMCID: PMC5717721 DOI: 10.1104/pp.17.01490] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 10/31/2017] [Indexed: 05/20/2023]
Abstract
Training for experimental plant biologists needs to combine bioinformatics, quantitative approaches, computational biology, and training in the art of collaboration, best achieved through fully integrated curriculum development.
Collapse
Affiliation(s)
- Joanna Friesner
- Agricultural Sustainability Institute and Department of Neurobiology, Physiology, and Behavior, University of California, Davis, California 95616
| | - Sarah M Assmann
- Biology Department, Penn State University, University Park, Pennsylvania 16802
| | - Ruth Bastow
- GARNet, School of Biosciences, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Jim Beynon
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Volker Brendel
- Department of Biology and Department of Computer Science, Indiana University, Bloomington, Indiana 47405
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Alexander Bucksch
- Department of Plant Biology, Warnell School of Forestry and Natural Resources, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | - Wolfgang Busch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, 1030 Vienna, Austria; Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Jose R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Colleen J Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695
| | | | - Pascal Falter-Braun
- Institute of Network Biology, Department of Environmental Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Malia A Gehan
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | | | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Rodrigo Gutierrez
- FONDAP Center for Genome Regulation, Millennium Nucleus Center for Plant Systems and Synthetic Biology, Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile 8331150
| | - Ute Kramer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, CNRS, INRA, Montpellier SupAgro, Université Montpellier, Institut de Biologie Intégrative des Plantes "Claude Grignon," Place Viala, 34060 Montpellier cedex, France
| | - Shisong Ma
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - R J Cody Markelz
- Department of Plant Biology, University of California, Davis, California 95616
| | - Molly Megraw
- Department of Botany and Plant Pathology, Department of Computer Science, and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132; Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211
| | - James A H Murray
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, Wales, United Kingdom
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Sue Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Roger Smith
- Syngenta Crop Protection, Research Triangle Park, North Carolina 27709
| | - Edgar P Spalding
- Department of Botany, University of Wisconsin, Madison, Wisconsin 53706
| | - Crispin Taylor
- American Society of Plant Biologists, Rockville, Maryland 20855
| | | | - Keiko U Torii
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, Washington 98195
| | - Chris Town
- J. Craig Venter Institute, Rockville, Maryland 20850
| | - Matthew Vaughn
- Life Sciences Computing, Texas Advanced Computing Center, Austin, Texas 78758
| | - Richard Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri 63130
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724; U.S. Department of Agriculture Agricultural Research Service, Ithaca, New York 14853
| | - Olivia Wilkins
- Department of Plant Science, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Cranos Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Siobhan M Brady
- Department of Plant Biology, Genome Center, University of California, Davis, California 95616
| |
Collapse
|
42
|
Ritchey LE, Su Z, Tang Y, Tack DC, Assmann SM, Bevilacqua PC. Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo. Nucleic Acids Res 2017. [PMID: 28637286 PMCID: PMC5737731 DOI: 10.1093/nar/gkx533] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage. We also present a variation of Structure-seq2 in which a biotinylated nucleotide is incorporated during reverse transcription, which greatly facilitates the protocol by eliminating two PAGE purification steps. We benchmark Structure-seq2 on both mRNA and rRNA structure in rice (Oryza sativa). We demonstrate that Structure-seq2 can lead to new biological insights. Our Structure-seq2 datasets uncover hidden breaks in chloroplast rRNA and identify a previously unreported N1-methyladenosine (m1A) in a nuclear-encoded Oryza sativa rRNA. Overall, Structure-seq2 is a rapid, sensitive, and unbiased method to probe RNA in vivo and genome-wide that facilitates new insights into RNA biology.
Collapse
Affiliation(s)
- Laura E Ritchey
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Zhao Su
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Yin Tang
- Bioinformatics and Genomics Graduate Program, Pennsylvania State University, University Park, PA 16802, USA
| | - David C Tack
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.,Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
43
|
Albert R, Acharya BR, Jeon BW, Zañudo JGT, Zhu M, Osman K, Assmann SM. A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loops. PLoS Biol 2017; 15:e2003451. [PMID: 28937978 PMCID: PMC5627951 DOI: 10.1371/journal.pbio.2003451] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/04/2017] [Accepted: 09/04/2017] [Indexed: 11/19/2022] Open
Abstract
Stomata, microscopic pores in leaf surfaces through which water loss and carbon dioxide uptake occur, are closed in response to drought by the phytohormone abscisic acid (ABA). This process is vital for drought tolerance and has been the topic of extensive experimental investigation in the last decades. Although a core signaling chain has been elucidated consisting of ABA binding to receptors, which alleviates negative regulation by protein phosphatases 2C (PP2Cs) of the protein kinase OPEN STOMATA 1 (OST1) and ultimately results in activation of anion channels, osmotic water loss, and stomatal closure, over 70 additional components have been identified, yet their relationships with each other and the core components are poorly elucidated. We integrated and processed hundreds of disparate observations regarding ABA signal transduction responses underlying stomatal closure into a network of 84 nodes and 156 edges and, as a result, established those relationships, including identification of a 36-node, strongly connected (feedback-rich) component as well as its in- and out-components. The network’s domination by a feedback-rich component may reflect a general feature of rapid signaling events. We developed a discrete dynamic model of this network and elucidated the effects of ABA plus knockout or constitutive activity of 79 nodes on both the outcome of the system (closure) and the status of all internal nodes. The model, with more than 1024 system states, is far from fully determined by the available data, yet model results agree with existing experiments in 82 cases and disagree in only 17 cases, a validation rate of 75%. Our results reveal nodes that could be engineered to impact stomatal closure in a controlled fashion and also provide over 140 novel predictions for which experimental data are currently lacking. Noting the paucity of wet-bench data regarding combinatorial effects of ABA and internal node activation, we experimentally confirmed several predictions of the model with regard to reactive oxygen species, cytosolic Ca2+ (Ca2+c), and heterotrimeric G-protein signaling. We analyzed dynamics-determining positive and negative feedback loops, thereby elucidating the attractor (dynamic behavior) repertoire of the system and the groups of nodes that determine each attractor. Based on this analysis, we predict the likely presence of a previously unrecognized feedback mechanism dependent on Ca2+c. This mechanism would provide model agreement with 10 additional experimental observations, for a validation rate of 85%. Our research underscores the importance of feedback regulation in generating robust and adaptable biological responses. The high validation rate of our model illustrates the advantages of discrete dynamic modeling for complex, nonlinear systems common in biology. Guard cells, located in pairs on the surface of plant leaves, circumscribe microscopic pores called stomata, through which plants take up gaseous carbon dioxide that will be fixed by photosynthesis into sugars. However, plants also inevitably lose water vapor to the atmosphere through open stomata. Under drought conditions, the plant hormone abscisic acid (ABA) causes volume changes in guard cells that result in stomatal closure, thereby restricting water loss. Given the paramount importance of drought tolerance for plant survival, it is important to understand the cellular mechanisms underlying guard cell response to ABA, and over 100 studies in the literature have addressed this topic. We synthesized this information into a network that contains 84 cellular components and 156 interactions between them and then applied logic-based analyses to predict how these components coordinately transduce the ABA signal. We identified several positive feedback loops and mutual inhibition loops that can lead to sustained activity of their constituent components in the presence, or absence, of ABA. Control of these loops, for example, by other stimuli present in the natural environment, may sensitize the system to ABA. We validated some of the novel predictions from our model with new experiments.
Collapse
Affiliation(s)
- Réka Albert
- Department of Physics, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail: (RA); (SMA)
| | - Biswa R. Acharya
- Biology Department, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Byeong Wook Jeon
- Biology Department, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Jorge G. T. Zañudo
- Department of Physics, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Mengmeng Zhu
- Biology Department, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Karim Osman
- Biology Department, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sarah M. Assmann
- Biology Department, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail: (RA); (SMA)
| |
Collapse
|
44
|
Assmann SM, Jegla T. Guard cell sensory systems: recent insights on stomatal responses to light, abscisic acid, and CO 2. Curr Opin Plant Biol 2016; 33:157-167. [PMID: 27518594 DOI: 10.1016/j.pbi.2016.07.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/29/2016] [Accepted: 07/06/2016] [Indexed: 05/18/2023]
Abstract
By controlling the opening and closure of the stomatal pores through which gas exchange occurs, guard cells regulate two of the most important plant physiological processes: photosynthesis and transpiration. Accordingly, guard cells have evolved exquisite sensory systems. Here we summarize recent literature on guard cell sensing of light, drought (via the phytohormone abscisic acid (ABA)), and CO2. New advances in our understanding of how guard cells satisfy the energetic and osmotic requirements of stomatal opening and utilize phosphorylation to regulate the anion channels and aquaporins involved in ABA-stimulated stomatal closure are highlighted. Omics and modeling approaches are providing new information that will ultimately allow an integrated understanding of guard cell physiology.
Collapse
Affiliation(s)
- Sarah M Assmann
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA 16802, United States.
| | - Timothy Jegla
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA 16802, United States; Huck Institutes of the Life Sciences, 201 Life Sciences Building, University Park, PA 16802, United States.
| |
Collapse
|
45
|
Abstract
Single-stranded RNA molecules fold into extraordinarily complicated secondary and tertiary structures as a result of intramolecular base pairing. In vivo, these RNA structures are not static. Instead, they are remodeled in response to changes in the prevailing physicochemical environment of the cell and as a result of intermolecular base pairing and interactions with RNA-binding proteins. Remarkable technical advances now allow us to probe RNA secondary structure at single-nucleotide resolution and genome-wide, both in vitro and in vivo. These data sets provide new glimpses into the RNA universe. Analyses of RNA structuromes in HIV, yeast, Arabidopsis, and mammalian cells and tissues have revealed regulatory effects of RNA structure on messenger RNA (mRNA) polyadenylation, splicing, translation, and turnover. Application of new methods for genome-wide identification of mRNA modifications, particularly methylation and pseudouridylation, has shown that the RNA "epitranscriptome" both influences and is influenced by RNA structure. In this review, we describe newly developed genome-wide RNA structure-probing methods and synthesize the information emerging from their application.
Collapse
Affiliation(s)
- Philip C Bevilacqua
- Department of Chemistry.,Department of Biochemistry and Molecular Biology.,Center for RNA Molecular Biology
| | | | - Zhao Su
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802;
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802;
| |
Collapse
|
46
|
Zhu M, Monroe JG, Suhail Y, Villiers F, Mullen J, Pater D, Hauser F, Jeon BW, Bader JS, Kwak JM, Schroeder JI, McKay JK, Assmann SM. Molecular and systems approaches towards drought-tolerant canola crops. New Phytol 2016; 210:1169-1189. [PMID: 26879345 DOI: 10.1111/nph.13866] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
1169 I. 1170 II. 1170 III. 1172 IV. 1176 V. 1181 VI. 1182 1183 References 1183 SUMMARY: Modern agriculture is facing multiple challenges including the necessity for a substantial increase in production to meet the needs of a burgeoning human population. Water shortage is a deleterious consequence of both population growth and climate change and is one of the most severe factors limiting global crop productivity. Brassica species, particularly canola varieties, are cultivated worldwide for edible oil, animal feed, and biodiesel, and suffer dramatic yield loss upon drought stress. The recent release of the Brassica napus genome supplies essential genetic information to facilitate identification of drought-related genes and provides new information for agricultural improvement in this species. Here we summarize current knowledge regarding drought responses of canola, including physiological and -omics effects of drought. We further discuss knowledge gained through translational biology based on discoveries in the closely related reference species Arabidopsis thaliana and through genetic strategies such as genome-wide association studies and analysis of natural variation. Knowledge of drought tolerance/resistance responses in canola together with research outcomes arising from new technologies and methodologies will inform novel strategies for improvement of drought tolerance and yield in this and other important crop species.
Collapse
Affiliation(s)
- Mengmeng Zhu
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - J Grey Monroe
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yasir Suhail
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Florent Villiers
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
| | - Jack Mullen
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Dianne Pater
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Felix Hauser
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - Byeong Wook Jeon
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| | - Joel S Bader
- Department of Biomedical Engineering, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- School of Medicine, The Johns Hopkins University, Baltimore, MD, 21205, USA
| | - June M Kwak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20740, USA
- Center for Plant Aging Research, Institute for Basic Science, Department of New Biology, DGIST, Daegu, 42988, Korea
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section, Food and Fuel for the 21st Century Center, University of California San Diego, La Jolla, CA, 92093-016, USA
| | - John K McKay
- Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, 80523, USA
| | - Sarah M Assmann
- Biology Department, Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
47
|
Ferrero-Serrano Á, Assmann SM. The α-subunit of the rice heterotrimeric G protein, RGA1, regulates drought tolerance during the vegetative phase in the dwarf rice mutant d1. J Exp Bot 2016; 67:3433-43. [PMID: 27194741 PMCID: PMC4892740 DOI: 10.1093/jxb/erw183] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Essential in the Green Revolution was the development of high-yielding dwarf varieties of rice (Oryza sativa L.), but their selection was not based on responses to water limitation. We studied physiological responses to progressive drought of the dwarf rice mutant, d1, in which the RGA1 gene, which encodes the GTP-binding α-subunit of the heterotrimeric G protein, is non-functional. Wild-type (WT) plants cease net carbon fixation 11 days after water is withheld, while d1 plants maintain net photosynthesis for an additional week. During drought, d1 plants exhibit greater stomatal conductance than the WT, but both genotypes exhibit the same transpirational water loss per unit leaf area. This is explained by a smaller driving force for water loss in d1 owing to its lower leaf temperatures, consistent with its more erect architecture. As drought becomes more severe, WT plants show an accelerated decline in photosynthesis, which may be exacerbated by the higher leaf temperatures in the WT. We thus show how a rice mutant with dwarf and erect leaves has a decreased susceptibility to water stress. Accordingly, it may be useful to incorporate RGA1 mutation in breeding or biotechnological strategies for development of drought-resistant rice.
Collapse
Affiliation(s)
- Ángel Ferrero-Serrano
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA 16802, USA
| |
Collapse
|
48
|
Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P. 50 years of Arabidopsis research: highlights and future directions. New Phytol 2016; 209:921-44. [PMID: 26465351 DOI: 10.1111/nph.13687] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/24/2015] [Indexed: 05/14/2023]
Abstract
922 I. 922 II. 922 III. 925 IV. 925 V. 926 VI. 927 VII. 928 VIII. 929 IX. 930 X. 931 XI. 932 XII. 933 XIII. Natural variation and genome-wide association studies 934 XIV. 934 XV. 935 XVI. 936 XVII. 937 937 References 937 SUMMARY: The year 2014 marked the 25(th) International Conference on Arabidopsis Research. In the 50 yr since the first International Conference on Arabidopsis Research, held in 1965 in Göttingen, Germany, > 54 000 papers that mention Arabidopsis thaliana in the title, abstract or keywords have been published. We present herein a citational network analysis of these papers, and touch on some of the important discoveries in plant biology that have been made in this powerful model system, and highlight how these discoveries have then had an impact in crop species. We also look to the future, highlighting some outstanding questions that can be readily addressed in Arabidopsis. Topics that are discussed include Arabidopsis reverse genetic resources, stock centers, databases and online tools, cell biology, development, hormones, plant immunity, signaling in response to abiotic stress, transporters, biosynthesis of cells walls and macromolecules such as starch and lipids, epigenetics and epigenomics, genome-wide association studies and natural variation, gene regulatory networks, modeling and systems biology, and synthetic biology.
Collapse
Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jose Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Sarah M Assmann
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | | | - Siobhan M Brady
- Department of Plant Biology, University of California, Davis, CA, 95616, USA
| | - Jelena Brkljacic
- Arabidopsis Biological Resource Center, The Ohio State University, Columbus, OH, 43210, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Vincent Colot
- Departement de Biologie École Normale Supérieure, Biologie Moleculaire des Organismes Photosynthetiques, F-75230, Paris, France
| | - Sean Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA
| | - Jeff Dangl
- Department of Biology and Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - David Ehrhardt
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Joanna D Friesner
- Department of Plant Biology, Agricultural Sustainability Institute, University of California, Davis, CA, 95616, USA
| | - Wolf B Frommer
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Erich Grotewold
- Center for Applied Plant Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Elliot Meyerowitz
- Division of Biology and Biological Engineering and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology, A-1030, Vienna, Austria
| | - Craig Pikaard
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Chris Somerville
- Energy Biosciences Institute, University of California, Berkeley, CA, 94704, USA
| | - Mark Stitt
- Metabolic Networks Department, Max Planck Institute for Molecular Plant Physiology, D-14476, Potsdam, Germany
| | - Keiko U Torii
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Jamie Waese
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter McCourt
- Department of Cell & Systems Biology/CAGEF, University of Toronto, Toronto, ON, M5S 3B2, Canada
| |
Collapse
|
49
|
Tang Y, Assmann SM, Bevilacqua PC. Protein Structure Is Related to RNA Structural Reactivity In Vivo. J Mol Biol 2016; 428:758-766. [DOI: 10.1016/j.jmb.2015.11.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/27/2015] [Accepted: 11/10/2015] [Indexed: 11/15/2022]
|
50
|
Zhu M, Jeon BW, Geng S, Yu Y, Balmant K, Chen S, Assmann SM. Preparation of Epidermal Peels and Guard Cell Protoplasts for Cellular, Electrophysiological, and -Omics Assays of Guard Cell Function. Methods Mol Biol 2016; 1363:89-121. [PMID: 26577784 DOI: 10.1007/978-1-4939-3115-6_9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Bioassays are commonly used to study stomatal phenotypes. There are multiple options in the choice of plant materials and species used for observation of stomatal and guard cell responses in vivo. Here, detailed procedures for bioassays of stomatal responses to abscisic acid (ABA) in Arabidopsis thaliana are described, including ABA promotion of stomatal closure, ABA inhibition of stomatal opening, and ABA promotion of reaction oxygen species (ROS) production in guard cells. We also include an example of a stomatal bioassay for the guard cell CO2 response using guard cell-enriched epidermal peels from Brassica napus. Highly pure preparations of guard cell protoplasts can be produced, which are also suitable for studies on guard cell signaling, as well as for studies on guard cell ion transport. Small-scale and large-scale guard cell protoplast preparations are commonly used for electrophysiological and -omics studies, respectively. We provide a procedure for small-scale guard cell protoplasting from A. thaliana. Additionally, a general protocol for large-scale preparation of guard cell protoplasts, with specifications for three different species, A. thaliana, B. napus, and Vicia faba is also provided.
Collapse
Affiliation(s)
- Mengmeng Zhu
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Byeong Wook Jeon
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Sisi Geng
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA
| | - Yunqing Yu
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA, 16802, USA
| | - Kelly Balmant
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA
| | - Sixue Chen
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institute, University of Florida, 2033 Mowry Road, Gainesville, FL, 32610, USA
| | - Sarah M Assmann
- Biology Department, Penn State University, 208 Mueller Laboratory, University Park, PA, 16802, USA.
| |
Collapse
|